diff options
Diffstat (limited to 'plip/exchange/xml.py')
| -rw-r--r-- | plip/exchange/xml.py | 285 |
1 files changed, 285 insertions, 0 deletions
diff --git a/plip/exchange/xml.py b/plip/exchange/xml.py new file mode 100644 index 0000000..a5eee21 --- /dev/null +++ b/plip/exchange/xml.py @@ -0,0 +1,285 @@ +from lxml import etree + +from urllib.request import urlopen + + +class XMLStorage: + """Generic class for storing XML data from PLIP XML files.""" + + def getdata(self, tree, location, force_string=False): + """Gets XML data from a specific element and handles types.""" + found = tree.xpath('%s/text()' % location) + if not found: + return None + else: + data = found[0] + if force_string: + return data + if data == 'True': + return True + elif data == 'False': + return False + else: + try: + return int(data) + except ValueError: + try: + return float(data) + except ValueError: + # It's a string + return data + + def getcoordinates(self, tree, location): + """Gets coordinates from a specific element in PLIP XML""" + return tuple(float(x) for x in tree.xpath('.//%s/*/text()' % location)) + + +class Interaction(XMLStorage): + """Stores information on a specific interaction type""" + + def __init__(self, interaction_part): + self.id = interaction_part.get('id') + self.resnr = self.getdata(interaction_part, 'resnr') + self.restype = self.getdata(interaction_part, 'restype', force_string=True) + self.reschain = self.getdata(interaction_part, 'reschain', force_string=True) + self.resnr_lig = self.getdata(interaction_part, 'resnr_lig') + self.restype_lig = self.getdata(interaction_part, 'restype_lig', force_string=True) + self.reschain_lig = self.getdata(interaction_part, 'reschain_lig', force_string=True) + self.ligcoo = self.getcoordinates(interaction_part, 'ligcoo') + self.protcoo = self.getcoordinates(interaction_part, 'protcoo') + + +class HydrophobicInteraction(Interaction): + """Stores information on a hydrophobic interaction""" + + def __init__(self, hydrophobic_part): + Interaction.__init__(self, hydrophobic_part) + self.dist = self.getdata(hydrophobic_part, 'dist') + self.ligcarbonidx = self.getdata(hydrophobic_part, 'ligcarbonidx') + self.protcarbonidx = self.getdata(hydrophobic_part, 'protcarbonidx') + + +class HydrogenBond(Interaction): + """Stores information on a hydrogen bond interaction""" + + def __init__(self, hbond_part): + Interaction.__init__(self, hbond_part) + self.sidechain = self.getdata(hbond_part, 'sidechain') + self.dist_h_a = self.getdata(hbond_part, 'dist_h-a') + self.dist_d_a = self.getdata(hbond_part, 'dist_d-a') + self.dist = self.dist_d_a + + self.don_angle = self.getdata(hbond_part, 'don_angle') + self.protisdon = self.getdata(hbond_part, 'protisdon') + self.donoridx = self.getdata(hbond_part, 'donoridx') + self.acceptoridx = self.getdata(hbond_part, 'acceptoridx') + self.donortype = self.getdata(hbond_part, 'donortype', force_string=True) + self.acceptortype = self.getdata(hbond_part, 'acceptortype', force_string=True) + + +class WaterBridge(Interaction): + """Stores information on a water bridge interaction""" + + def __init__(self, wbridge_part): + Interaction.__init__(self, wbridge_part) + self.dist_a_w = self.getdata(wbridge_part, 'dist_a-w') + self.dist_d_w = self.getdata(wbridge_part, 'dist_d-w') + self.don_angle = self.getdata(wbridge_part, 'don_angle') + self.water_angle = self.getdata(wbridge_part, 'water_angle') + self.protisdon = self.getdata(wbridge_part, 'protisdon') + self.dist = self.dist_a_w if self.protisdon else self.dist_d_w + + self.donor_idx = self.getdata(wbridge_part, 'donor_idx') + self.acceptor_idx = self.getdata(wbridge_part, 'acceptor_idx') + self.donortype = self.getdata(wbridge_part, 'donortype', force_string=True) + self.acceptortype = self.getdata(wbridge_part, 'acceptortype', force_string=True) + self.water_idx = self.getdata(wbridge_part, 'water_idx') + self.watercoo = self.getcoordinates(wbridge_part, 'watercoo') + + +class SaltBridge(Interaction): + """Stores information on a salt bridge interaction""" + + def __init__(self, sbridge_part): + Interaction.__init__(self, sbridge_part) + self.dist = self.getdata(sbridge_part, 'dist') + self.protispos = self.getdata(sbridge_part, 'protispos') + self.lig_group = self.getdata(sbridge_part, 'lig_group', force_string=True) + self.lig_idx_list = [int(tagpart.text) for tagpart in + sbridge_part.xpath('lig_idx_list/idx')] + + +class PiStacking(Interaction): + """Stores information on a pi stacking interaction""" + + def __init__(self, pistack_part): + Interaction.__init__(self, pistack_part) + self.centdist = self.getdata(pistack_part, 'centdist') + self.dist = self.centdist + self.angle = self.getdata(pistack_part, 'angle') + self.offset = self.getdata(pistack_part, 'offset') + self.type = self.getdata(pistack_part, 'type') + self.lig_idx_list = [int(tagpart.text) for tagpart in + pistack_part.xpath('lig_idx_list/idx')] + + +class PiCation(Interaction): + """Stores information on a pi cation interaction""" + + def __init__(self, pication_part): + Interaction.__init__(self, pication_part) + self.dist = self.getdata(pication_part, 'dist') + self.offset = self.getdata(pication_part, 'offset') + self.protcharged = self.getdata(pication_part, 'protcharged') + self.lig_group = self.getdata(pication_part, 'lig_group') + self.lig_idx_list = [int(tag.text) for tag in pication_part.xpath('.//lig_idx_list/idx')] + + +class HalogenBond(Interaction): + """Stores information on a halogen bond interaction""" + + def __init__(self, halogen_part): + Interaction.__init__(self, halogen_part) + self.dist = self.getdata(halogen_part, 'dist') + self.don_angle = self.getdata(halogen_part, 'don_angle') + self.acc_angle = self.getdata(halogen_part, 'acc_angle') + self.donortype = self.getdata(halogen_part, 'donortype', force_string=True) + self.acceptortype = self.getdata(halogen_part, 'acceptortype', force_string=True) + self.don_idx = self.getdata(halogen_part, 'don_idx') + self.acc_idx = self.getdata(halogen_part, 'acc_idx') + self.sidechain = self.getdata(halogen_part, 'sidechain') + + +class MetalComplex(Interaction): + """Stores information on a metal complexe interaction""" + + def __init__(self, metalcomplex_part): + Interaction.__init__(self, metalcomplex_part) + self.metal_idx = self.getdata(metalcomplex_part, 'metal_idx') + self.metal_type = self.getdata(metalcomplex_part, 'metal_type', force_string=True) + self.target_idx = self.getdata(metalcomplex_part, 'target_idx') + self.target_type = self.getdata(metalcomplex_part, 'target_type', force_string=True) + self.coordination = self.getdata(metalcomplex_part, 'coordination') + self.dist = self.getdata(metalcomplex_part, 'dist') + self.location = self.getdata(metalcomplex_part, 'location', force_string=True) + self.rms = self.getdata(metalcomplex_part, 'rms') + self.geometry = self.getdata(metalcomplex_part, 'geometry', force_string=True) + self.complexnum = self.getdata(metalcomplex_part, 'complexnum') + self.targetcoo = self.getcoordinates(metalcomplex_part, 'targetcoo') + self.metalcoo = self.getcoordinates(metalcomplex_part, 'metalcoo') + + +class BSite(XMLStorage): + """Stores all information about an specific binding site.""" + + def __init__(self, bindingsite, pdbid): + self.bindingsite = bindingsite + self.pdbid = pdbid + self.bsid = ":".join(bindingsite.xpath('identifiers/*/text()')[2:5]) + self.uniqueid = ":".join([self.pdbid, self.bsid]) + self.hetid = self.getdata(bindingsite, 'identifiers/hetid', force_string=True) + self.longname = self.getdata(bindingsite, 'identifiers/longname', force_string=True) + self.ligtype = self.getdata(bindingsite, 'identifiers/ligtype', force_string=True) + self.smiles = self.getdata(bindingsite, 'identifiers/smiles', force_string=True) + self.inchikey = self.getdata(bindingsite, 'identifiers/inchikey', force_string=True) + self.position = self.getdata(bindingsite, 'identifiers/position') + self.chain = self.getdata(bindingsite, 'identifiers/chain', force_string=True) + + # Information on binding site members + self.members = [] + for member in bindingsite.xpath('identifiers/members/member'): + self.members += member.xpath('text()') + + self.composite = self.getdata(bindingsite, 'identifiers/composite') + + # Ligand Properties + self.heavy_atoms = self.getdata(bindingsite, 'lig_properties/num_heavy_atoms') + self.hbd = self.getdata(bindingsite, 'lig_properties/num_hbd') + self.unpaired_hbd = self.getdata(bindingsite, 'lig_properties/num_unpaired_hbd') + self.hba = self.getdata(bindingsite, 'lig_properties/num_hba') + self.unpaired_hba = self.getdata(bindingsite, 'lig_properties/num_unpaired_hba') + self.hal = self.getdata(bindingsite, 'lig_properties/num_hal') + self.unpaired_hal = self.getdata(bindingsite, 'lig_properties/num_unpaired_hal') + self.molweight = self.getdata(bindingsite, 'lig_properties/molweight') + self.logp = self.getdata(bindingsite, 'lig_properties/logp') + self.rotatable_bonds = self.getdata(bindingsite, 'lig_properties/num_rotatable_bonds') + self.rings = self.getdata(bindingsite, 'lig_properties/num_aromatic_rings') + + # Binding Site residues + self.bs_res = [] + for tagpart in bindingsite.xpath('bs_residues/bs_residue'): + resnumber, reschain = tagpart.text[:-1], tagpart.text[-1] + aa, contact, min_dist = tagpart.get('aa'), tagpart.get('contact'), tagpart.get('min_dist') + new_bs_res = {'resnr': int(resnumber), 'reschain': reschain, 'aa': aa, + 'contact': True if contact == 'True' else False, 'min_dist': float(min_dist)} + self.bs_res.append(new_bs_res) + + # Interacting chains + self.interacting_chains = [] + for chain in bindingsite.xpath('interacting_chains/interacting_chain'): + self.interacting_chains += chain.xpath('text()') + + # Interactions + interactions = bindingsite.xpath('interactions')[0] + self.hydrophobics = [HydrophobicInteraction(x) for x in + interactions.xpath('hydrophobic_interactions/hydrophobic_interaction')] + self.hbonds = [HydrogenBond(x) for x in interactions.xpath('hydrogen_bonds/hydrogen_bond')] + self.wbridges = [WaterBridge(x) for x in interactions.xpath('water_bridges/water_bridge')] + self.sbridges = [SaltBridge(x) for x in interactions.xpath('salt_bridges/salt_bridge')] + self.pi_stacks = [PiStacking(x) for x in interactions.xpath('pi_stacks/pi_stack')] + self.pi_cations = [PiCation(x) for x in interactions.xpath('pi_cation_interactions/pi_cation_interaction')] + self.halogens = [HalogenBond(x) for x in interactions.xpath('halogen_bonds/halogen_bond')] + self.metal_complexes = [MetalComplex(x) for x in interactions.xpath('metal_complexes/metal_complex')] + self.num_contacts = len(self.hydrophobics) + len(self.hbonds) + len(self.wbridges) + len(self.sbridges) + \ + len(self.pi_stacks) + len(self.pi_cations) + len(self.halogens) + len(self.metal_complexes) + self.has_interactions = self.num_contacts > 0 + + self.get_atom_mapping() + self.counts = self.get_counts() + + def get_atom_mapping(self): + """Parses the ligand atom mapping.""" + # Atom mappings + smiles_to_pdb_mapping = self.bindingsite.xpath('mappings/smiles_to_pdb/text()') + if not smiles_to_pdb_mapping: + self.mappings = {'smiles_to_pdb': None, 'pdb_to_smiles': None} + else: + smiles_to_pdb_mapping = {int(y[0]): int(y[1]) for y in [x.split(':') + for x in smiles_to_pdb_mapping[0].split(',')]} + self.mappings = {'smiles_to_pdb': smiles_to_pdb_mapping} + self.mappings['pdb_to_smiles'] = {v: k for k, v in self.mappings['smiles_to_pdb'].items()} + + def get_counts(self): + """counts the interaction types and backbone hydrogen bonding in a binding site""" + + hbondsback = len([hb for hb in self.hbonds if not hb.sidechain]) + counts = {'hydrophobics': len(self.hydrophobics), 'hbonds': len(self.hbonds), + 'wbridges': len(self.wbridges), 'sbridges': len(self.sbridges), 'pistacks': len(self.pi_stacks), + 'pications': len(self.pi_cations), 'halogens': len(self.halogens), 'metal': len(self.metal_complexes), + 'hbond_back': hbondsback, 'hbond_nonback': (len(self.hbonds) - hbondsback)} + counts['total'] = counts['hydrophobics'] + counts['hbonds'] + counts['wbridges'] + \ + counts['sbridges'] + counts['pistacks'] + counts['pications'] + counts['halogens'] + counts['metal'] + return counts + + +class PlipXML(XMLStorage): + """Parses and stores all information from a PLIP XML file.""" + + def __init__(self, xmlfile): + self.load_data(xmlfile) + + # Parse general information + self.version = self.getdata(self.doc, '/report/plipversion/') + self.pdbid = self.getdata(self.doc, '/report/pdbid', force_string=True) + self.filetype = self.getdata(self.doc, '/report/filetype') + self.fixed = self.getdata(self.doc, '/report/pdbfixes/') + self.filename = self.getdata(self.doc, '/report/filename') + self.excluded = self.doc.xpath('/report/excluded_ligands/excluded_ligand/text()') + + # Parse binding site information + self.bsites = {BSite(bs, self.pdbid).bsid: BSite(bs, self.pdbid) for bs in self.doc.xpath('//bindingsite')} + self.num_bsites = len(self.bsites) + + def load_data(self, xmlfile): + """Loads/parses an XML file and saves it as a tree if successful.""" + self.doc = etree.parse(xmlfile)
\ No newline at end of file |